Willow Creek Academy (WCA) received its charter in 2001 and opened its doors in September 2001 as a K-4 school with 37 students, just 19% of all district kids.

[citation needed] SMCSD officials stated that year that some area wealthy families decided to go back to public school due to the existence of Willow Creek.

[5] The office of the Attorney General of California had accused the Sausalito Marin City district of racially discriminating by keeping the two different schools open.

[9] In 2020 the estimated price of what would be needed to fix the Willow Creek facilities to the point where they are best maintained was $40 million.

[9] Parents were encouraged to participate in their children's education and the school community by driving on field trips, volunteering in the classroom, campus clean-up days and creek restoration projects.

[15] Willow Creek attributed the 2012 reduction to rapid growth and has stated that the school's goal is to surpass a cumulative score of 900.

The school's per-student spending has been declining for the past several years, and the funding are filled by grants and other private fundraising, including the Willow Creek Foundation (WCF).

WCF is a not-for-profit foundation that was set up to support WCA and educational choice for Sausalito and Marin City families.

In mid-2019, the Sausalito Marin City School District (SMCSD) drastically cut WCA's budget, by around 30%.

[18] As of spring 2013, the student body was 37% Hispanic, 25% White, 18% African-American, 11% Asian, 1% Native Hawaiian or Pacific Islander, and 8% who self-identify as multi-ethnic.